Did one of these on Biohaze, I'll just reuse.
Definitely a tough choice, especially with all the great characters in Mikami-san's titles. But I had to go back to some of my better times playing games and one a bit more obscure, especially then. Tatsuya Suou from Persona 2 Tsumi (Main Character) / Batsu (Supporting Character).
First off, especially at that time, RPG's were fairly cliche. Games like Soul Hackers and Persona were twisted bottles of fun in a market otherwise lead by wooden sword wielding eight-year-olds. The main character of Persona 2 is a senior in high school who is taken in by a very twisted fate. In short, the character is a quiet young man who is very serious about priorities that are important to him. These being factors beyond the typical age groups standard. Always deep in thought, though keeping most of it inside, he says what needs to be said at the right time. Some can mistake this for a cold attitude, though those close to him know it is anything but. He always does the right thing and expresses utmost care in dire situations. This in part with the various decisions the game allows the player to make (right down to sexual orientation) and it leaves a very young but mature mark, something I feel I can personally relate to.
Edit: And by the way, I love Persona 2's art style. Completely unique and not one bit typical anime. It was really just too good. P3/4's is definitely beautiful, but not as out of the box as P2's.